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Crystal structure of the bromodomain 1 in mouse Brd4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS PDB ENTRY 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 3.6M Na formate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.014 α = 90 b = 47.442 β = 90 c = 78.024 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2009-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 19.6 99.4 0.076 15.35 18865 18865 -3 -3 25.811
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.6 99.5 0.409 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OSS 1.55 19.6 18865 18855 961 99.45 0.184 0.186 0.184 0.1902 0.219 0.2338 RANDOM 18.5
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 6.28 -3.57 -2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_sphericity_free 14.672 r_dihedral_angle_4_deg 14.272 r_dihedral_angle_3_deg 13.267 r_sphericity_bonded 9.737 r_scangle_it 6.295 r_dihedral_angle_1_deg 5.823 r_scbond_it 4.944 r_mcangle_it 3.598 r_rigid_bond_restr 3.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_sphericity_free 14.672 r_dihedral_angle_4_deg 14.272 r_dihedral_angle_3_deg 13.267 r_sphericity_bonded 9.737 r_scangle_it 6.295 r_dihedral_angle_1_deg 5.823 r_scbond_it 4.944 r_mcangle_it 3.598 r_rigid_bond_restr 3.312 r_mcbond_it 2.9 r_angle_refined_deg 2.239 r_mcbond_other 1.754 r_angle_other_deg 1.227 r_xyhbond_nbd_refined 0.275 r_symmetry_vdw_other 0.269 r_nbd_refined 0.231 r_nbtor_refined 0.196 r_nbd_other 0.188 r_chiral_restr 0.152 r_symmetry_hbond_refined 0.148 r_symmetry_vdw_refined 0.138 r_nbtor_other 0.104 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction MOLREP phasing